Research Project Description
Adverse Outcome Pathway (AOP) Knowledgebase
Research Participation Program
Office of Research and Development
National Health and Environmental Effects Research Laboratory
U.S. Environmental Protection Agency
Research Triangle Park, NC
A postdoctoral research project training opportunity is currently available at the U.S. Environmental Protection Agency (EPA), National Health and Environmental Effects Research Laboratory (NHEERL), Integrated Systems Toxicology Division (ISTD) in Research Triangle Park, North Carolina.
The EPA and the Joint Research Centre of the European Commission have jointly proposed to develop an Adverse Outcome Pathway (AOP) knowledgebase (KB) as part of a broader Organization for Economic Cooperation and Development (OECD) effort to define and formalize AOPs (http://www.epa.gov/research/priorities/docs/aop-wiki.pdf). As a co-developer of this research project, the EPA is responsible for maintaining a wiki to house draft AOP information and for developing tools that will integrate the wiki with other components of the AOPKB, such as the Effectopedia repository. In addition, this research project will provide information to support EPA modeling projects such as Virtual Tissues (http://www.epa.gov/ncct/virtual_tissues/what.html).
The research participant will have an opportunity to write programs that merge information entered into the AOP wiki with other data sources (such as information extracted from the scientific literature and biological relationships inferred from genomics data) to create formal descriptions of biological processes suitable for computational modeling. S/he will participate in defining AOPs and establishing essential characteristics of this conceptual framework. S/he will be evaluating AOPs being entered into the AOP wiki and providing feedback to wiki users on constructive changes to better formalize their AOPs. Major research activities may include:
- programming in Ruby and R;
- reading and interpreting relevant scientific literature;
- curating entries in the AOP knowledgebase;
- interacting with computational modelers to define data/information needs;
- presenting at professional meetings; and
- authoring manuscripts for publication in peer-reviewed journals.
The research participant will be collaborating on an international AOPKB development project and will interact with top scientists in this field from around the world. S/he will be encouraged to publish in peer-reviewed journals and to present research results at local and national meetings.
This training research represents an excellent opportunity for an aspiring computational biologist. A research participant entering with a background in computer science will learn about biological processes underlying disease. A research participant with a strong biological background will learn programming skills directly applicable for both data mining and mechanistic modeling approaches. The research participant will become proficient in the Ruby and R programming languages, both of which are very common in computational and systems biology. S/he will collaborate with experts in HTS, Omics and dynamic modeling of virtual systems. This, combined with the programming skills they will develop, should make it possible for them to move into any of these areas or continue down a transdisciplinary path at their discretion.
Applicants must have received a doctoral degree in bioinformatics, systems biology, computer science, or a closely related field within five years of the desired starting date, or completion of all requirements for the degree should be expected prior to the starting date. Experience with computer programming, computational modeling or formal descriptions of biological processes, and statistics is desirable.
The program is open to all qualified individuals without regard to race, sex, religion, color, age, physical or mental disability, national origin, or status as a Vietnam era or disabled veteran. U.S. citizenship or lawful permanent resident status is preferred (but can also hold an appropriate visa status, however, an H1B visa is not appropriate).
The appointment is full-time for one year and may be renewed for up to two additional years upon recommendation of EPA contingent on the availability of funds. The participant will receive a monthly stipend. Funding may be made available to reimburse the participant’s travel expenses to present the results of his/her research at scientific conferences. No funding will be made available to cover costs for pre-appointment visits, relocation costs, tuition and fees, or a participant's health insurance. The participant must show proof of health and medical insurance. This can be obtained through ORISE. The participant does not become an EPA employee.
The contact for this project is Stephen Edwards. He can be contacted at email@example.com.
How to Apply:
An application can be found at http://orise.orau.gov/epa/applicants/application.htm. Please reference Project # EPA-ORD/NHEERL-ISTD-2013-04 when calling or writing for information.